I think part of the fun of playing Ganondorf, is that sometimes you just have to make some nutty reads, or go for risky ****. Ultimate is a faster game, and therefore you can do more crazy stuff with Ganondorf in neutral. There's no real way for a beefy guy like him to deal with fast characters well. Albeit, Nair and fast fall seems really good for controlling the space in front of him, I tend to do that often myself.
As for zoners, it's a pain in the ass, but that's where your patience is tested. There's not a lot of options against projectiles, you either just try to avoid them or move in with shield, and both those options are scary for him. But all you need is just one throw, or flame choke to get started on your mix ups, and zoning gets hard for the other player once Ganondorf is in their face.